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- What's new ?
+ What's new in Jalview 2.10.2 ?
- Jalview 2.9 has been in development since December 2014. In addition
- to a multitude of bug fixes and minor improvements (both small, and
- rather big!), it also brings major new capabilities for codon-level
- analysis of protein alignments and the retrieval and manipulation of
- structural data.
For the full list of changes, see the
- Jalview 2.9 Release Notes.
+ Full details about Jalview 2.10.2 are in the Release Notes, but the
+ highlights are below.
+
+ - Update to JABAWS 2.2
Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by JABAWS 2.2.
+ Several of the programs provided as services have been updated, so
+ their options and parameters have changed.
+ - New preferences for opening
+ web pages for database cross-references via the UK Elixir's
+ EMBL-EBI's MIRIAM database and identifiers.org services.
+
+
- Highlights in Jalview 2.9
+ Experimental Features
+
+
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the Tools→Enable
+ Experimental Features option, and then restart Jalview.
+
- - Visualisation, editing and analysis of
- cDNA and Protein alignments
A new Split View window allows linked
- protein and nucleotide sequence alignments to be viewed, edited,
- and analysed as one.
cDNA alignments can also be
- reconstructed from protein alignments calculated by Jalview's web
- services, and update in response to edits in the amino acid view.
To
- start experimenting with cDNA/Protein analysis, jut drop a file
- containing cDNA sequences which code for, and have IDs matching
- proteins in an existing alignment, and Jalview will do the rest.
- - Enhanced Integration of UCSF Chimera
Jalview
- 2.9 provides full support for the use of Chimera to view 3D
- structures linked to alignment views in the Jalview Desktop. We've
- also included support for saving Chimera sessions in Jalview
- project files.
Jalview and Chimera communicate using local
- web server connections, which may cause firewall alerts on some
- systems, but has the advantage of allowing bidirectional
- communication. Communication between Jalview and Chimera is now
- much more responsive, and selected regions in Chimera are now
- shown as highlighted regions in the Jalview desktop.
- - Interactive querying of the PDBe
Jalview
- users can now browse and retrieve 3D structure data from the PDB
- via the PDBe
- Search API (Gutmanas
- et al 2014). Developed in collaboration with the PDBe group at
- EMBL-EBI, the interface allows both structured and free-text
- queries to be performed, and allows automatic selection of the
- most relevant structures for an alignment acording to a variety of
- criteria.
- - Improved support for RNA visualisation
Jalview
- 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views
- can also now be stored in Jalview projects. We've also dealt with
- a number of lingering bugs in the VARNA/Jalview interface,
- including the loss of pseudoknots when RNA secondary structure is
- shown VARNA.
- - Protein Secondary Structure predictions
- with JPred4Jalview includes a number of new features for working
- with secondary structure predictions from the JPred4 server. These
- include the ability to automatically hide insertions and highlight
- mutations in an alignment with respect to a reference sequence.
- Jalview 2.9's new scrollable SVG HTML export mode was also
- developed specifically for the JPred4 server.
+ - Annotation transfer between Chimera and Jalview
Two
+ new entries in
+ the Chimera viewer's Chimera menu allow positional annotation to
+ be exchanged between Chimera and Jalview.
-